Enemy Mine: Karai wants to team up with the Turtles against the Kraang. After what she did in "The Alien Agenda", she has a hard time convincing them. Interestingly, they are the ones who double-cross her.
Foreshadowing: The Kraang ship doesn't explode after being shot down, just sinks into the harbor. Shredder also manages to capture one of the Kraang.
He Knows Too Much: The Kraang ship goes after the Turtles because of their knowledge of the Kraang.
Hypocrite: Karai calls Leo out on taking advantage of their friendship to double-cross her, ignoring that she did the exact same thing in "The Alien Agenda".
Not quite the exact same thing. Karai was nothing but honest about being untrustworthy in that episode, agreeing with Raph rather than Leo about being "bad news". She never made Leo any promises not to betray their alliance, while Leo did with her.
Also, something really should be said about how after all the discussion of if they could trust Karai, the Turtles end up double-crossing her.
Made of Iron: While everything else that gets hit by the Kraang ship's beam immediately explodes, the Shellraiser stands up to a prolonged shot and can still operate after (though dialogue indicates it was heavily damaged).
Nice Job Breaking It, Hero: The Turtles attempt to take advantage of their deal with Karai to assassinate the Shredder ruins any chance of getting her on their side. Though as Raph points out, given that she's his daughter(which she neglected to tell the turtles) there was no guarantee that she wouldn't have turned on them anyways.
Not So Different: Karai accuses Leo for being just as short sighted and obsessive as Shredder.
Power Creep, Power Seep: The Turtles fare a lot better against Shredder this time. While they don't actually land a blow, they also manage to avoid any serious injury.
Granted this time they did what they could to avoid getting too close to him for too long.
Revenge Before Reason: Once again we see Shredder showing shades of this. Karai claims Leo is no better when he goes back on their deal by trying to defeat Shredder.